Dear David,
>
> Thanks. Ok! Could you help me understand how can I write the command line for eddy without topup step? Eddy talking about compulsory arguments, but I don't know if I have all compulsory files to fill all blanks of eddy command line:
>
> The following COMPULSORY options have not been set:
> --imain (Ok! it's just uncorrected image)
> --mask (Ok! brain mask obtained on bet step)
> --index File containing indices for all volumes in --imain into --acqp and --topup (I don't know how to make this!)
> --acqp File containing acquisition parameters (I don't know how obtain thin either!)
> --bvecs File containing the b-vectors for all volumes in --imain (ok! I have this)
> --bvals File containing the b-values for all volumes in --imain (ok! I have this)
> --out Basename for output (ok! just a basename)
if you take a look at https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy/Faq you should be able to figure out what your acqparams.txt and your index.txt should look like.
>
>
>> If you have some other way of estimating the susceptibility-induced field (e.g. a traditional fieldmap) you can pass that to eddy using the --field option.
>
> I will love to make this but how? I will send a list of files extracted from DICOM file. Any of those files can do the job?
>
> Files:
>
> 3Plane_Loc.nii.gz
> 3Plane_Loca.nii.gz
> 3Plane_Locb.nii.gz
> Average_DC.nii.gz
> Ax_DTI.bval
> Ax_DTI.bvec
> Ax_DTI.nii.gz
> Fractional_Aniso..nii.gz
> Sag_CUBE_flair.nii.gz
> Sag_T1_3D.nii.gz
> fMRI_Rest.nii.gz
>
I am afraid I don’t see anything there that looks like a fieldmap. In order to get a fieldmap you need to explicitly run a fieldmap sequence as part of your experiment.
>
>>>
>>> Another question is:
>>>
>>> Looking on documentation at https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide there have the necessary steps to processing DTI data using FDT. Steps 1 and 2 are ok. But step 3 says that its needed to do a dtifit before topup (step 4) and eddy correction (step 5) and after that another dtifit (step 6). So the corrections on steps 4 and 5 are made on fitted data obtained on step 3 and not on original dwi data?
>
>> I don’t quite understand this. When I look at the page you have linked to I don’t recognise the numbering you describe nor the instructions.
>
> I attached a screenshot showing the part I talking about
I see. The first dtifit is run _only_ to make sure that the bvecs are in the correct format for FSL. You only use it to visualise the V1 file in fslview and ensure that the lines line up between voxels. Once you have done that you can throw away the output from the first run of dtifit and proceed as if you had never run it.
Jesper
>
>
> Thank you very much
>
> Regards
>
> David
>
>> Jesper
>
>>>
>>> Thank you
>>>
>>> Best Reagards
>>>
>>> David
> <fdt.png>
|